The 19 genomes of Drosophila: A BAC library resource for genus-wide and genome-scale comparative evolutionary research

Genetics

Volumn 187, Issue 4, 2011, Pages 1023-1030

  Song, Xiang ^a   Goicoechea, Jose Luis ^a   Ammiraju, Jetty S S ^a   Luo, Meizhong ^a   He, Ruifeng ^a   Lin, Jinke ^a   Lee, So Jeong ^a   Sisneros, Nicholas ^a   Watts, Tom ^b   Kudrna, David A ^a   Golser, Wolfgang ^a   Ashley, Elizabeth ^a   Collura, Kristi ^a   Braidotti, Michele ^a   Yu, Yeisoo ^a   Matzkin, Luciano M ^b,c   McAllister, Bryant F ^d   Markow, Therese Ann ^b,c   Wing, Rod A ^a  

^a UNIVERSITY OF ARIZONA   (United States)

^b University of Arizona   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CLONE; COMPARATIVE STUDY; DROSOPHILA; ECOLOGY; GENE LIBRARY; GENE MAPPING; GENE REARRANGEMENT; GENETIC VARIABILITY; GENETICS; GENOME; MOLECULAR EVOLUTION; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL;

ANIMALS; BIOLOGICAL EVOLUTION; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, INSECT; DROSOPHILA MELANOGASTER; GENES, INSECT; GENOME, INSECT; GENOMIC LIBRARY; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ANIMALIA; BACTERIA (MICROORGANISMS); DROSOPHILA MELANOGASTER; HEXAPODA;

EID: 79955446773     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.111.126540     Document Type: Article

References (53)

1. Adams, M.D., S.E. Celniker, R.A. Holt, C.A. Evans, J.D. Gocayne et al., 2000 The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Ammiraju, J.S., M. Luo, J.L. Goicoechea, W. Wang, D. Kudrna et al., 2006. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res. 16: 140-147.
3. Anderson, W.W., J. Arnold, D. G. Baldwin, A.T. Beckenbach, C.J. Brown et al., 1991 Four decades of inversion polymorphism in Drosophila pseudoobscura. Proc. Natl. Acad. Sci. USA 88: 10367-10371.
4. Bosco, G., P. Campbell, J. T. Leiva-Neto and T.A. Markow, 2007 Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 177: 1277-1290.
5. Celniker, S.E., D.A. Wheeler, B. Kronmiller, J.W. Carlson, A. Halpern et al., 2002 Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 3: research0079.1-0079.14.
6. Charlesworth, B., D. Charlesworth, J. Hnilicka, A. Yu and D.S. Guttman, 1997 Lack of degeneration of loci on the neo-Y chromosome of Drosophila americana. Genetics 145: 989-1002.
7. Drosophila 12 Genomes Consortium, 2007 Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
8. Eichler, E.E., and P.J. Dejong, 2002 Biomedical applications and studies of molecular evolution: a proposal for a primate genomic library resource. Genome Res. 12: 673-678.
9. Ellison, C.K., and K.L. Shaw, 2010 Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness. BMC Genomics 11: 428-436.
10. Evans, A.L., P.A. Mena and B.F. Mcallister, 2007 Positive selection near an inversion breakpoint on the neo-X chromosome of Drosophila americana. Genetics 177: 1303-1319.
11. Fang, G., B.P. Blackmon, D.C. Henry, M. E. Staton, C.A. Saski et al., 2010 Genomic tools development for Aquilegia: construction of a BAC-based physical map. BMC Genomics 11: 621-628.
12. Gibbs, R.A., G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren et al., 2003 Genome sequence of the Brown Norway rat yields insights intomammalian evolution. Nature 428: 493-521.
13. Gilbert, D. G., 2007 DroSpeGe: rapid access database for new Drosophila species genomes. Nucleic Acids Res. 35: D480-D485.
14. Gonzalez, J., M. Nefedov, I. Bosdet, F. Casals, O. Calvete et al., 2005 A BAC-based physical map of the Drosophila buzzatii genome. Genome Res. 15: 885-892.
15. Gregory, S.G., M. Sekhon, J. Schein, S. Zhao, K. Osoegawa et al., 2002 A physicalmap of the mouse genome. Nature 418: 743-750.
16. Gregory, T.R., 2005 Synergy between sequence and size in largescale genomics. Nat. Rev. Genet. 6: 699-708.
17. Gregory, T.R., and J.S. Johnston, 2008 Genome size diversity in the family Drosophilidae. Heredity 101: 228-238.
18. Havlak, P., R. Chen, K.J. Durbin, A. Egan, Y. Ren et al., 2004 The Atlas genome assembly system. Genome Res. 14: 721-732.
19. Hoskins, R.A., C.R. Nelson, B.P. Berman, T.R. Laverty, R.A. George et al., 2000 A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science 287: 2271-2274.
20. International Human Genome Mapping Consortium, 2000a A physical map of the human genome. Nature 409: 934-941.
21. International Human Genome Mapping Consortium, 2000b Initial sequencing and analysis of the human genome. Nature 409: 860-921.
22. Kim, H., B. Hurwitz, Y. Yu, K. Collura, M. Gill et al., 2008 Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol. 9: R45.
23. Kim, U.J., B.W. Birren, T. Slepak, V. Mancina, C. Boysen et al., 1996 Construction and characterization of a human bacterial artificial chromosome library. Genomics 34: 213-218.
24. Krzywinske, M., J. Wallis, C. Gosele, I. Bosdet, R. Chiu et al., 2004 Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 14: 766-779.
25. Leung, W., C.D. Shaffer, T. Cordonnier, J. Wong, M. S. Itano et al., 2010 Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Genetics 185: 1519-1534.
26. Locke, J., L. Podemski, N. Aippersbach, H. Kemp and R. Hodgetts, 2000 A physical map of the polytenized region (101EF-102F) of chromosome 4 in Drosophila melanogaster. Genetics 155: 1175-1183.
27. Luo, M., and R.A. Wing, 2003 An improved method for plant BAC library construction, pp. 3-20 in Plant Functional Genomics, edited by E. Grotewold. Humana Press, Totowa, NJ.
28. Luo, M., H. Kim, D. Kudrna, N.B. Sisneros, S. Lee et al., 2006 Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. BMC Genomics 7: 106.
29. Luo, M.C., C. Thomas, F.M. You, J. Hsiao, S. Ouyang et al., 2003 High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378-389.
30. Markow, T.A., and P.M. O'Grady, 2006 Evolutionary genetics of reproductive behavior in Drosophila: connecting the dots. Annu. Rev. Genet. 39: 263-291.
31. Markow, T.A., and P.M. O'Grady, 2007 Drosophila biology in the genomic age. Genetics 177: 1269-1276.
32. Mateos, M., S.J. Castrezana, B.J. Nnakivell, A.M. Estes, T.A. Markow et al., 2006 Heritable endosymbionts of Drosophila. Genetics 174: 363-376.
33. Murakami, K., A. Toyoda, M. Hattori, Y. Kuroki, A. Fujiyama et al., 2008 BAC library construction and BAC end sequencing of five Drosophila species: the comparative map with the D. melanogaster genome. Genes Genet. Syst. 83: 245-246.
34. Myers, E.W., G.G. Sutton, A.L. Delcher, I.M. Dew, D.P. Fasulo et al., 2000 A whole-genome assembly of Drosophila. Science 287: 2196-2204.
35. Osoegawa, K., A.M. Tateno, P.Y. Woon, E. Frengen, A.G. Mammoser et al., 2000 Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. Genome Res. 10: 116-128.
36. Osoegawa, K., A.G. Mammoser, C. Wu, E. Frengen, C. Zeng et al., 2001 A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 11: 483-496.
37. Osoegawa, K., B. Zhu, C.L. Shu, T. Ren, Q. Cao et al., 2004 BAC resources for the rat genome project. Genome Res. 14: 780-785.
38. Osoegawa, K., G.M. Vessere, C.L. Shu, R.A. Hoskins, J.P. Abad et al., 2007 BAC clones generated from sheared DNA. Genomics 89: 291-299.
39. Orr, H. A., and J. A. Coyne, 1989 The genetics of postzygotic isolation in the Drosophila virilis group. Genetics 121: 527-537.
40. Pitnick, S., T. A. Markow and G. S. Spicer, 1995 Delayed male maturity is a cost of producing large sperm in Drosophila. Proc. Natl. Acad. Sci. USA 92: 10614-10618.
41. Popadic, A., and W. W. Anderson, 1994 The history of a genetic system. Proc. Natl. Acad. Sci. USA 91: 6819-6823.
42. Powell, J. R., 1997 Progress and Prospects in Evolutionary Biology: The Drosophila Model. Oxford University Press, London/New York/Oxford.
43. Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky et al., 2005. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, geni, and cis-element evolution. Genome Res. 15: 1-18.
44. Rubin, G. M., and E. B. Lewis, 2000 A brief history of Drosophila's contributions to genome research. Science 287: 2216-2218.
45. Schaeffer, S. W., A. Bhutkar, B. F. Mcallister, M. Matsuda, L.M. Matzkin et al., 2008 Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics 179: 1601-1655.
46. Soderlund, C., S. Humphray, A. Dunham and L. French, 2000 Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10: 1772-1787.
47. Stark, A., M. F. Lin, P. Kheradpour, J. S. Pedersen, L. Parts et al., 2007 Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-232.
48. Sweigart, A. L., 2010 Simple Y-autosomal incompatibilities cause hybrid male sterility in reciprocal crosses between Drosophila virilis and D. americana. Genetics 184: 779-787.
49. Venken, K. J. T., and H. J. Bellen, 2007 Transgenesis upgrades for Drosophila melanogaster. Development 134: 3571-3584.
50. Venken, K. J. T., Y. He, R. A. Hoskins and H. J. Bellen, 2006 P[acman]: a BAC transgenic platformfor targeted insertion of large DNA fragments in D. melanogaster. Science 314: 1747-1751.
51. Venken, K. J. T., J. W. Carlson, K. L. Schulze, H. Pan, Y. He et al., 2009 Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat. Methods 6: 431-434.
52. Vieira, J., C. P. Vieira, D. L. Hartl and E. R. Lozovskaya, 1997 Discordant rates of chromosome evolution in the Drosophila virilis species group. Genetics 147: 223-230.
53. Wicker, T., E. Schlagenhauf, A. Graner, T. J. Close, B. Keller et al., 2006. 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7: 275.